Hierarchical analysis of RNA secondary structures with pseudoknots based on sections
Fig 6
Optimization of weighting parameter for 3-cluster pseudoknot structure prediction.
Prediction accuracy metrics (sensitivity and positive predictive value) as a function of weight parameter w applied to the free energy contribution of latter section pairs in the weighted energy minimization approach. Optimal performance occurs at w = 0.8, indicating preferential weighting of former section pair interactions while maintaining contribution from latter pairs in type-1 3-cluster configurations.